5 research outputs found
Additional file 1 of readat: An R package for reading and working with SomaLogic ADAT files
R source package of readat at the time of publication
Effect of induced hypoglycemia on inflammation and oxidative stress in type 2 diabetes and control subjects
Intensive diabetes control has been associated with increased mortality in type 2 diabetes (T2DM); this has been suggested to be due to increased hypoglycemia. We measured hypoglycemia-induced changes in endothelial parameters, oxidative stress markers and inflammation at baseline and after a 24-hour period in type 2 diabetic (T2DM) subjects versus age-matched controls. Case-control study: 10 T2DM and 8 control subjects. Blood glucose was reduced from 5 (90 mg/dl) to hypoglycemic levels of 2.8 mmol/L (50 mg/dl) for 1 hour by incremental hyperinsulinemic clamps using baseline and 24 hour samples. Measures of endothelial parameters, oxidative stress and inflammation at baseline and at 24-hours post hypoglycemia were performed: proteomic (Somalogic) analysis for inflammatory markers complemented by C-reactive protein (hsCRP) measurement, and proteomic markers and urinary isoprostanes for oxidative measures, together with endothelial function. Between baseline and 24 -hours after hypoglycemia, 15 of 140 inflammatory proteins differed in T2DM whilst only 1 of 140 differed in controls; all returned to baseline at 24-hours. However, elevated hsCRP levels were seen at 24-hours in T2DM (2.4 mg/L (1.2–5.4) vs. 3.9 mg/L (1.8–6.1), Baseline vs 24-hours, P Other Information Published in: Scientific Reports License: https://creativecommons.org/licenses/by/4.0See article on publisher's website: http://dx.doi.org/10.1038/s41598-020-61531-z</p
Adaptation of a Commonly Used, Chemically Defined Medium for Human Embryonic Stem Cells to Stable Isotope Labeling with Amino Acids in Cell Culture
Metabolic
labeling with stable isotopes is a prominent technique
for comparative quantitative proteomics, and stable isotope labeling
with amino acids in cell culture (SILAC) is the most commonly used
approach. SILAC is, however, traditionally limited to simple tissue
culture regimens and only rarely employed in the context of complex
culturing conditions as those required for human embryonic stem cells
(hESCs). Classic hESC culture is based on the use of mouse embryonic
fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic
contamination, contribution of unlabeled amino acids by the feeders,
interlaboratory variability of MEF preparation, and the overall complexity
of the culture system are all of concern in conjunction with SILAC.
We demonstrate a feeder-free SILAC culture system based on a customized
version of a commonly used, chemically defined hESC medium developed
by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a
trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies
(Vancouver, Canada)]. This medium, together with adjustments to the
culturing protocol, facilitates reproducible labeling that is easily
scalable to the protein amounts required by proteomic work flows.
It greatly enhances the usability of quantitative proteomics as a
tool for the study of mechanisms underlying hESCs differentiation
and self-renewal. Associated data have been deposited to the ProteomeXchange
with the identifier PXD000151
Adaptation of a Commonly Used, Chemically Defined Medium for Human Embryonic Stem Cells to Stable Isotope Labeling with Amino Acids in Cell Culture
Metabolic
labeling with stable isotopes is a prominent technique
for comparative quantitative proteomics, and stable isotope labeling
with amino acids in cell culture (SILAC) is the most commonly used
approach. SILAC is, however, traditionally limited to simple tissue
culture regimens and only rarely employed in the context of complex
culturing conditions as those required for human embryonic stem cells
(hESCs). Classic hESC culture is based on the use of mouse embryonic
fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic
contamination, contribution of unlabeled amino acids by the feeders,
interlaboratory variability of MEF preparation, and the overall complexity
of the culture system are all of concern in conjunction with SILAC.
We demonstrate a feeder-free SILAC culture system based on a customized
version of a commonly used, chemically defined hESC medium developed
by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a
trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies
(Vancouver, Canada)]. This medium, together with adjustments to the
culturing protocol, facilitates reproducible labeling that is easily
scalable to the protein amounts required by proteomic work flows.
It greatly enhances the usability of quantitative proteomics as a
tool for the study of mechanisms underlying hESCs differentiation
and self-renewal. Associated data have been deposited to the ProteomeXchange
with the identifier PXD000151
Epigenetics meets proteomics in an epigenome-wide association study with circulating blood plasma protein traits
DNA methylation and blood circulating proteins have been associated with many complex disorders, but the underlying disease-causing mechanisms often remain unclear. Here, we report an epigenome-wide association study of 1123 proteins from 944 participants of the KORA population study and replication in a multi-ethnic cohort of 344 individuals. We identify 98 CpG-protein associations (pQTMs) at a stringent Bonferroni level of significance. Overlapping associations with transcriptomics, metabolomics, and clinical endpoints suggest implication of processes related to chronic low-grade inflammation, including a network involving methylation of NLRC5, a regulator of the inflammasome, and associated pQTMs implicating key proteins of the immune system, such as CD48, CD163, CXCL10, CXCL11, LAG3, FCGR3B, and B2M. Our study links DNA methylation to disease endpoints via intermediate proteomics phenotypes and identifies correlative networks that may eventually be targeted in a personalized approach of chronic low-grade inflammation.Other Information Published in: Nature Communications License: https://creativecommons.org/licenses/by/4.0See article on publisher's website: http://dx.doi.org/10.1038/s41467-019-13831-w</p